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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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Error information for different fast5 files: Not in alignment sam 1095 #44

Open Bessyyi opened 3 years ago

Bessyyi commented 3 years ago

Hi teacher ! I'm trying to call DNA modifications by using deepmod.However,i get the problem 'Error information for different fast5 files: Not in alignment sam 1095'.Can you give me some advice about this error? What's more ,what's the fast5 data you input?.The sequence of motif ?Why i input raw data , i get a few methylation coverage?

NC_008261.1 649 650 A 74 - 649 650 0,0,0 74 0 0 NC_008261.1 651 652 A 65 - 651 652 0,0,0 65 0 0 NC_008261.1 652 653 A 79 - 652 653 0,0,0 79 0 0 NC_008261.1 656 657 A 77 - 656 657 0,0,0 77 0 0 NC_008261.1 658 659 A 73 - 658 659 0,0,0 73 0 0 NC_008261.1 661 662 A 65 - 661 662 0,0,0 65 0 0 NC_008261.1 662 663 A 81 - 662 663 0,0,0 81 0 0 NC_008261.1 663 664 A 75 - 663 664 0,0,0 75 0 0 NC_008261.1 682 683 A 78 - 682 683 0,0,0 78 0 0 NC_008261.1 715 716 A 79 - 715 716 0,0,0 79 1 1 NC_008261.1 721 722 A 73 - 721 722 0,0,0 73 0 0 NC_008261.1 724 725 A 72 - 724 725 0,0,0 72 0 0 NC_008261.1 726 727 A 79 - 726 727 0,0,0 79 6 5 NC_008261.1 730 731 A 55 - 730 731 0,0,0 55 0 0 NC_008261.1 734 735 A 72 - 734 735 0,0,0 72 1 1 NC_008261.1 736 737 A 69 - 736 737 0,0,0 69 0 0 NC_008261.1 738 739 A 82 - 738 739 0,0,0 82 0 0 NC_008261.1 741 742 A 74 - 741 742 0,0,0 74 0 0 NC_008261.1 742 743 A 85 - 742 743 0,0,0 85 0 0 NC_008261.1 744 745 A 53 - 744 745 0,0,0 53 0 0 NC_008261.1 748 749 A 79 - 748 749 0,0,0 79 0 0 NC_008261.1 751 752 A 83 - 751 752 0,0,0 83 0 0 NC_008261.1 756 757 A 80 - 756 757 0,0,0 80 0 0 NC_008261.1 758 759 A 82 - 758 759 0,0,0 82 0 0 NC_008261.1 763 764 A 70 - 763 764 0,0,0 70 0 0 NC_008261.1 767 768 A 73 - 767 768 0,0,0 73 0 0 NC_008261.1 768 769 A 82 - 768 769 0,0,0 82 0 0 NC_008261.1 772 773 A 75 - 772 773 0,0,0 75 0 0 NC_008261.1 775 776 A 67 - 775 776 0,0,0 67 0 0

liuqianhn commented 2 years ago

@Bessyyi sorry for the late reply.

  1. Some sequences cannot be aligned against a reference genome, and thus are reported as "not in alignment". If you have a smaller fraction of such reads, it is fine.
  2. The input of DeepMod is the fast5 files with basecalling info, reference genomes and a motif from users.
  3. I have no clue for lower modification percentage here unless you describe more about your testing data and its basecalling info.